对SNP加权,贝叶斯式和机器学习模型进行比较评估,用于霍尔斯坦牛的基因组预测
Weijie Zheng1, Qi Zhang1, Jinfeng He1
1Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
BMC genomics
|November 12, 2025
概括
基因组最佳线性无偏预测 (GBLUP) 模型可以通过结合SNP权重来改进. 虽然先进的方法显示出前景,但传统的贝叶斯模型提供了最佳的准确性,GBLUP平衡了实际动物育种的效率和准确性.
科学领域:
- 动物育种和遗传学动物育种和遗传学
- 基因组预测 基因组预测
- 统计基因组学 统计基因组学
背景情况:
- 基因组最佳线性无偏预测 (GBLUP) 假设SNP贡献相同,限制准确性.
- 通过SNP先验来增强预测框架对于动物繁殖至关重要.
研究的目的:
- 开发和评估包含SNP权重的新型基因组预测模型.
- 将新模型的准确性和计算效率与现有方法进行比较.
主要方法:
- 对16122只荷尔斯坦牛的122,672个SNP进行了分析,对9个特征进行了分析.
- 开发了动态先前注意神经网络 (DPAnet) 和SNP加权的GBLUP (WGBLUP),使用GWAS和BayesBπ的SNP权重.
- 使用交叉验证对GBLUP,贝叶斯方法,SVR和KRR进行基准模型.
主要成果:
- 对于特定的特征,DPAnet比GBLUP提高了准确性 (例如,FP的3.0%).
- 贝叶斯模型,特别是BayesR,实现了最高的平均精度 (0.625).
- 先进的方法在计算上是密集的,需要超过GBLUP.UP的六倍时间.
结论:
- 贝叶斯R提供了最高的预测性能,而GBLUP提供了准确性和效率的平衡.
- 权重模型显示出潜力,但目前传统贝叶斯模型的表现优于传统贝叶斯模型.
- 未来对因果SNP的识别可能会提高加权模型的性能.
相关概念视频
Comparing Copy Number Variations and SNPs
18.5K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.5K
Single Nucleotide Polymorphisms-SNPs
17.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
17.9K
Genome-wide Association Studies-GWAS
15.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
15.3K
Pharmacokinetic Models: Comparison and Selection Criterion
319
Physiological and compartmental models are valuable tools used in studying biological systems. These models rely on differential equations to maintain mass balance within the system, ensuring an accurate representation of the dynamic processes at play.
Physiological models take a detailed approach by considering specific molecular processes. They can predict drug distribution, metabolism, and elimination changes, providing a comprehensive understanding of how drugs interact with the body.
Physiological models take a detailed approach by considering specific molecular processes. They can predict drug distribution, metabolism, and elimination changes, providing a comprehensive understanding of how drugs interact with the body.
319
Evolutionary Relationships through Genome Comparisons
6.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.8K
Heritability
569
Heritability is a statistical concept that measures the degree to which genetic differences among individuals contribute to trait variations within a population. It is a fundamental idea in genetics, often prone to misinterpretation. Heritability is expressed as a percentage, reflecting the proportion of variation in a specific trait across a population that can be linked to genetic differences. However, it's important to understand that heritability does not determine how "genetic"...
569


